I am not a tax expert, and I properly don't know what I'm talking about, but want to offer my opinion since you have not received a response from the community. I am assuming that the LLC and your personal finances/taxes are kept separately and that the material receipts you have recently found are for the items purchased with personal funds.
In my opinion, the LLC gross revenue would include all the direct construction loan payments and the LLC material deductions would include all material purchased through the company accounts plus the reimbursement checks that the company paid to you. These checks are not income, they offset your expense. You cannot deduct the cost of the material you purchased with personal funds on your personal taxes but should keep the purchase records to show these payments to you are not part of your personal income. You can, of course, deduct the interest paid on the construction loan on schedule A of your personal taxes (subject to limits).
The basis in your new home is the total of the funds borrowed on the construction loan which covers all the cost of labor, materials, and permits. If your reimbursement was less than your expense, the difference should have been added to your home’s basis and deducted from LLC income on your personal taxes. If your reimbursement was more than your expense, the difference should have been subtracted from your home’s basis and your LLC income should have been increased by that amount on your personal taxes.
With the discovery of additional personal construction material receipts, your personal taxes for 2022 and 2023 should be amended to reflect a reduction of taxable LLC income by the difference between the total amount of personal funds spent on construction material and the total amount reimbursed.
Bottom Line: I vote for option 1.
